Understanding how genes are differentially regulated during the development of an organism is a fundamental problem in biology. Genetic studies of maize have provided many examples of programmed changes in gene expression during development and have identified regulatory phenomena such as the effects of transposable elements on gene expression and paramutation. One such genetically characterized locus in maize is B, which regulates the expression of the purple anthocyanin pigments in the plant. Variation in the developmental timing and tissue-specificity of anthocyanin synthesis is determined by which allele is present at B. Examining different B alleles at the molecular level should reveal nucleotide sequences responsible for regulating the timing and tissue- specificity of pigment production. Certain B alleles undergo or promote paramutation: a heritable alteration in gene expression promoted by the presence of two specific alleles in the same plant. Many models have been proposed to explain paramutation, including gene conversion, alterations in chromatin structure, DNA modification, or the interaction or transposition of DNA elements. A molecular description of this allelic interaction should reveal general principles on cell heritable regulation of gene expression as it occurs during development. These principles should be applicable to other organisms where a combined genetic and molecular approach is not yet feasible. The long term goals are to examine the molecular mechanisms controlling the expression of B. The specific aim of this proposal is to clone the B genomic sequences using transposable elements and to use the cloned sequences and mutants to begin analyzing the structure and function of B. Multiple independent insertion mutants and revertants have been isolated. The mutants and revertants isolated from them, have varied phenotypes with respect to the tissues in which pigment is synthesized. The insertion of an element into B will produce a molecular marker that segregates with the mutant phenotype. The element and the adjacent gene will be recovered by taking advantage of the homology between the element inserted into the B gene and the cloned transposable element. The cloned sequences will then be used to determine the structure and expression of the wild type and mutant B alleles as well as the molecular basis for paramutation.